LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# 2d indenter simulation

dimension	2
boundary	p s p

atom_style	atomic
neighbor	0.3 bin
neigh_modify	delay 5

# create geometry

lattice		hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region		box block 0 20 0 10 -0.25 0.25
create_box	2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
  2 by 2 by 1 MPI processor grid
create_atoms	1 box
Created 420 atoms
  Time spent = 0.00031352 secs

mass		1 1.0
mass		2 1.0

# LJ potentials

pair_style	lj/cut 2.5
pair_coeff	* * 1.0 1.0 2.5

# define groups

region	        1 block INF INF INF 1.25 INF INF
group		lower region 1
60 atoms in group lower
group		mobile subtract all lower
360 atoms in group mobile
set		group lower type 2
  60 settings made for type

# initial velocities

compute	  	new mobile temp
velocity	mobile create 0.2 482748 temp new
fix		1 all nve
fix		2 lower setforce 0.0 0.0 0.0
fix		3 all temp/rescale 100 0.1 0.1 0.01 1.0

# run with indenter

timestep	0.003
variable	k equal 1000.0/xlat
variable        y equal "13.0*ylat - step*dt*0.02*ylat"

fix		4 all indent $k sphere 10 v_y 0 5.0
fix		4 all indent 882.849286914813 sphere 10 v_y 0 5.0
fix		5 all enforce2d

thermo		1000
thermo_modify	temp new
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)

#dump		1 all atom 250 dump.indent

#dump		2 all image 1000 image.*.jpg type type #		zoom 1.6 adiam 1.5
#dump_modify	2 pad 5

#dump		3 all movie 1000 movie.mpg type type #		zoom 1.6 adiam 1.5
#dump_modify	3 pad 5

run		30000
Neighbor list info ...
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 17 15 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.047 | 3.047 | 3.047 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
       0          0.2   -3.1727576            0   -3.0018052    -1.436185    444.53333 
    1000   0.11573595   -3.0964873            0   -2.9975606  -0.20448672    441.83732 
    2000   0.11519605   -3.0960246            0   -2.9975594  -0.38133491    442.33058 
    3000   0.11367906   -3.0839597            0   -2.9867912  -0.42579765    444.59119 
    4000   0.11618844   -3.0860897            0   -2.9867762 -0.041580916    439.84614 
    5000   0.11327789   -3.0848614            0   -2.9880358  -0.48898867    446.19202 
    6000   0.12058424   -3.0869438            0    -2.983873  0.011477134    440.56887 
    7000   0.11772522   -3.0833477            0   -2.9827207 -0.090378245    442.56787 
    8000   0.12533514   -3.0970033            0   -2.9898715   0.13263189    441.23478 
    9000    0.1198683   -3.0867062            0   -2.9842473   0.34046664     439.4706 
   10000   0.12234014   -3.0835007            0   -2.9789291   0.28399731    441.94307 
   11000   0.11082436   -3.0754796            0   -2.9807511   0.62194284    441.32012 
   12000    0.1084272   -3.0646379            0   -2.9719584   0.65383569    442.64668 
   13000   0.11686417   -3.0600388            0   -2.9601477    1.0041123    438.50135 
   14000   0.12557378   -3.0570017            0    -2.949666   0.85709169    442.10189 
   15000   0.11934084   -3.0498848            0   -2.9478768    1.0392201    451.74396 
   16000   0.12576913    -3.045218            0   -2.9377154    1.3479479     441.2702 
   17000   0.11546579   -3.0348367            0   -2.9361409     1.631821    439.48441 
   18000   0.12148869   -3.0221152            0   -2.9182713    1.6088855    449.25443 
   19000   0.11883863   -3.0036777            0    -2.902099    1.5201108    447.12736 
   20000   0.11163567   -3.0038144            0   -2.9083924    1.4078554    461.76339 
   21000   0.11361999   -2.9900869            0   -2.8929688    1.1334192    473.91362 
   22000   0.12696379   -3.0207381            0   -2.9122143   0.83288039    473.02925 
   23000    0.1188706     -3.01731            0    -2.915704    1.1482286    468.57874 
   24000   0.11820885   -3.0098527            0   -2.9088123   0.98884958    472.75675 
   25000   0.11671309   -3.0101308            0   -2.9103689    1.2402973    469.77097 
   26000   0.11965934   -3.0091118            0   -2.9068315   0.94844832    469.04458 
   27000   0.12147721   -3.0085715            0   -2.9047374    1.2363584    474.98572 
   28000   0.11718062    -2.993818            0   -2.8936565     1.143781    478.94786 
   29000   0.10922042   -2.9873887            0   -2.8940313    1.6184815    473.13968 
   30000   0.11475456   -2.9749758            0    -2.876888    1.8682946    472.49357 
Loop time of 1.15893 on 4 procs for 30000 steps with 420 atoms

Performance: 6709635.246 tau/day, 25885.938 timesteps/s
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.39848    | 0.4603     | 0.53798    |   8.6 | 39.72
Neigh   | 0.018286   | 0.020391   | 0.022765   |   1.4 |  1.76
Comm    | 0.18903    | 0.27493    | 0.34712    |  13.2 | 23.72
Output  | 0.00055623 | 0.00077116 | 0.0014129  |   0.0 |  0.07
Modify  | 0.28166    | 0.29302    | 0.30362    |   1.5 | 25.28
Other   |            | 0.1095     |            |       |  9.45

Nlocal:    105 ave 115 max 90 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost:    96.25 ave 104 max 87 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs:    931.25 ave 1078 max 743 min
Histogram: 1 0 1 0 0 0 0 0 0 2

Total # of neighbors = 3725
Ave neighs/atom = 8.86905
Neighbor list builds = 608
Dangerous builds = 0

# run without indenter

unfix           4
run		30000
Per MPI rank memory allocation (min/avg/max) = 3.047 | 3.048 | 3.048 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
   30000   0.11475456   -2.9749758            0    -2.876888    1.8675667    472.67773 
   31000   0.11574891   -3.0442299            0   -2.9452921  -0.72600606    489.16618 
   32000   0.11316772   -3.0299575            0    -2.933226  -0.74912451    483.50803 
   33000   0.12321675    -3.052617            0    -2.947296   0.29368262    473.07336 
   34000   0.11671309   -3.0470741            0   -2.9473122  -0.46988097    480.59621 
   35000   0.11671309   -3.0456501            0   -2.9458882  -0.74504498    475.07349 
   36000   0.11980973   -3.0797043            0   -2.9772955  0.083053833    461.14624 
   37000   0.10992033   -3.0712499            0   -2.9772942   -0.6447083     468.1598 
   38000   0.11831288   -3.0676136            0   -2.9664842  -0.59676518    469.61724 
   39000   0.11663782   -3.0775961            0   -2.9778985   0.21776888    460.87504 
   40000   0.10805913   -3.0688733            0   -2.9765084  -0.59632811    469.15555 
   41000   0.12118734   -3.0800988            0   -2.9765125  -0.32401944    466.81124 
   42000   0.12373313   -3.0822746            0   -2.9765123 -0.0033603954    462.85792 
   43000    0.1078275   -3.0686759            0    -2.976509  -0.71758451    469.60392 
   44000   0.12315017   -3.0787716            0   -2.9735076  -0.05619902    463.06786 
   45000   0.11564078   -3.0833684            0   -2.9845231  -0.36953273    465.92986 
   46000   0.10640706   -3.0654913            0   -2.9745386  -0.53685976     469.3539 
   47000   0.11810977   -3.0754985            0   -2.9745428  0.088083121    463.20699 
   48000   0.11241387   -3.0828874            0   -2.9868003  -0.54828531    466.25548 
   49000   0.11679121   -3.0748686            0   -2.9750399  -0.33781022    465.50451 
   50000   0.11656344     -3.07471            0   -2.9750761 -0.054088803    461.22814 
   51000   0.12060058   -3.0781622            0   -2.9750774  -0.55815121    468.81379 
   52000   0.11936306   -3.0876851            0   -2.9856581  -0.34773758    464.10154 
   53000   0.11032135   -3.0799138            0   -2.9856153   -0.1735616      465.533 
   54000   0.12365261   -3.0737021            0   -2.9680086  -0.52954909    468.29003 
   55000   0.12763641   -3.0771061            0   -2.9680074  -0.17884875    464.79749 
   56000   0.12638245   -3.0879132            0   -2.9798863   -0.2754242    464.35767 
   57000   0.11481136   -3.0780176            0   -2.9798812  -0.45547532    468.09393 
   58000   0.11858604   -3.0812503            0   -2.9798874  -0.17502776     463.2168 
   59000   0.11344551   -3.0768536            0   -2.9798847  -0.32382437    465.29204 
   60000   0.11637998   -3.0793607            0   -2.9798836  -0.45942931    466.04868 
Loop time of 0.903556 on 4 procs for 30000 steps with 420 atoms

Performance: 8605992.311 tau/day, 33202.131 timesteps/s
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.3899     | 0.45567    | 0.53041    |   8.7 | 50.43
Neigh   | 0.017401   | 0.021048   | 0.024747   |   2.1 |  2.33
Comm    | 0.17915    | 0.26432    | 0.34168    |  13.8 | 29.25
Output  | 0.00051928 | 0.00093985 | 0.0021935  |   0.0 |  0.10
Modify  | 0.067609   | 0.075224   | 0.08228    |   2.4 |  8.33
Other   |            | 0.08635    |            |       |  9.56

Nlocal:    105 ave 112 max 98 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost:    92.5 ave 96 max 89 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs:    892.25 ave 1003 max 788 min
Histogram: 2 0 0 0 0 0 0 0 1 1

Total # of neighbors = 3569
Ave neighs/atom = 8.49762
Neighbor list builds = 634
Dangerous builds = 0
Total wall time: 0:00:02
